Ahmed Awan
11d4a9165a
[25.0] Rerun workflows for the correct version/instance
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In `GET /api/workflows/{encoded_workflow_id}/download`, for the case when `instance = True`, we were correctly obtaining the stored workflow.
However, then in `WorkflowContentsManager.workflow_to_dict` we were not considering the case that when `instance = True`, we need to not return the `latest_workflow.workflow_to_dict`, and instead return the specific workflow instance which has been specified.
We did handle the case when `version` is explicitly provided here, but not instance.
Fixes https://github.com/galaxyproject/galaxy/issues/20223
2025-05-20 13:46:51 -05:00
mvdbeek
a92286ba8e
Merge branch 'release_24.2' into release_25.0
2025-05-19 17:00:12 +02:00
mvdbeek
957f6f5475
Merge branch 'release_24.1' into release_24.2
2025-05-19 16:54:19 +02:00
Marius van den Beek
c4605dad00
Merge pull request #20239 from natefoo/fix-ucsc-display-as
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[24.1] Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL
2025-05-19 16:52:44 +02:00
Marius van den Beek
e5af55199b
Merge pull request #20281 from mvdbeek/httpx
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[25.0] Add non-dev httpx dependency
2025-05-19 16:08:16 +02:00
mvdbeek
50ec064838
Add non-dev httpx dependency
2025-05-19 15:19:33 +02:00
Martin Cech
3df96589c9
Merge branch 'release_24.2' into release_25.0
2025-05-19 12:44:44 +02:00
Martin Cech
1f7f2e7845
Merge branch 'release_24.1' into release_24.2
2025-05-19 12:44:19 +02:00
Martin Cech
4e1acd06ce
Merge branch 'release_24.0' into release_24.1
2025-05-19 12:43:58 +02:00
Martin Cech
faa7442ee7
Merge branch 'release_23.2' into release_24.0
2025-05-19 12:43:20 +02:00
Martin Cech
7d4b3de58f
Merge branch 'release_23.1' into release_23.2
2025-05-19 12:32:42 +02:00
Marius van den Beek
e2ad28d9c8
Merge pull request #20266 from mvdbeek/extend_custom_tool_schema
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[25.0] Add more descriptions to custom tool source schema
2025-05-19 10:45:25 +02:00
mvdbeek
0e13bacee5
Provide more field annotations
2025-05-17 18:58:15 +02:00
Ahmed Awan
669e4d54f5
Update version to 25.0.rc1
2025-05-16 12:07:36 -05:00
Ahmed Awan
db80c5c03e
Add 25.0 migration tags
2025-05-16 11:45:19 -05:00
Marius van den Beek
dcfa9bb8cd
Merge pull request #20260 from common-workflow-lab/metadata-CONVERTER_tar_to_directory
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Fix tool-provided metadata for CONVERTER_tar_to_directory
2025-05-16 16:52:32 +02:00
mvdbeek
a4bad06a06
Merge branch 'release_24.2' into dev
2025-05-16 16:24:49 +02:00
mvdbeek
2156e2d98e
Merge branch 'release_24.1' into release_24.2
2025-05-16 16:23:56 +02:00
mvdbeek
9a0d482f1a
Merge branch 'release_24.0' into release_24.1
2025-05-16 16:23:36 +02:00
Nicola Soranzo
663c08aec4
Fix tool-provided metadata for CONVERTER_tar_to_directory
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The metadata are in the "default" (not "legacy") format, so need to
use a newer tool profile.
Also:
- Use CDATA and `&&` in command
2025-05-16 15:13:16 +02:00
mvdbeek
3eaa78b745
Fix job rerun for dynamic tools
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Fixes https://github.com/galaxyproject/galaxy/issues/20255
2025-05-16 12:17:42 +02:00
mvdbeek
65df554439
Fall back to name in job summary if no input label given
2025-05-16 11:07:41 +02:00
Nate Coraor
94721e3ec5
Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL
2025-05-15 12:24:49 -04:00
Dannon
2cf27ac352
Merge branch 'dev' into anvil-theme
2025-05-15 10:55:23 -04:00
mvdbeek
fd392b805a
Fix test_charts_h5web, drop test_charts_nvd3_bar since there's no nvd3_bar anymore
2025-05-15 14:19:13 +02:00
mvdbeek
93f081d1c2
Selenium test fixes
2025-05-15 14:19:13 +02:00
mvdbeek
83de984f07
Move /api/datatypes/{datatype} to avoid conflict
2025-05-14 20:39:05 +02:00
mvdbeek
f628ee230e
Wait for ... to disappear
2025-05-14 20:37:30 +02:00
mvdbeek
0e7ee07cac
Keep using history panel item edit button in selenium
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New tab needs to be disabled if dataset is running, can follow up later.
2025-05-14 20:37:29 +02:00
mvdbeek
ce0e0f6b24
Selenium fixes
2025-05-14 20:37:28 +02:00
Dannon Baker
a0220694ee
Drop all-datatypes visualization mapping endpoint
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We have this for edam data, formats, sniffers, etc., though. It's a
pattern we should make a decision on -- these may be better implemented
as a set of requested keys on the main datatypes summary and exposed
independently on the datatype detail endpoint that has been added.
2025-05-14 08:50:34 -04:00
Dannon Baker
85c55ac094
Drop unused import
2025-05-14 08:50:34 -04:00
Dannon Baker
764dbcde8f
Add default visualization plugins for GeoJSON and VitessceJSON datatypes; include TIFF viewer for TIFF datatype
2025-05-14 08:50:34 -04:00
Dannon Baker
4d5d834327
Drop 'default_params' concept for preferred viz, for now -- this is extra admin/configuration burden without much benefit at this point
2025-05-14 08:50:34 -04:00
Dannon Baker
8111f85ab2
Don't load top-level visualization_mappings in datatypes_conf -- we pushed these to indivdual datatypes.
2025-05-14 08:50:34 -04:00
Dannon Baker
6bbf6321fa
Swap configuration of default dataset viz to be specified inline with the datatype.
2025-05-14 08:50:34 -04:00
Dannon Baker
f8c739efde
Adds a new /api/datatypes/{datatype} endpoint
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provides comprehensive information about a specific datatype in a single
response, consolidating information previously spread across multiple
endpoints, and adds a bit new.
2025-05-14 08:50:33 -04:00
Dannon Baker
47ca870ae4
Adjust datatypes preferred viz API /datatypes/{type}/visualizations
2025-05-14 08:50:33 -04:00
Dannon Baker
a1ce48a282
Preferred viz rough sketch
2025-05-14 08:50:33 -04:00
Dannon Baker
959b8bd00b
Sketch out initial dataset view component
2025-05-14 08:32:21 -04:00
Dannon
eac679df74
Merge pull request #20100 from ahmedhamidawan/enhance_external_login
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Enhance external login interface styling
2025-05-14 08:20:25 -04:00
Dannon
8e3501aff7
Merge pull request #19786 from ahmedhamidawan/make_private_make_history_inaccessible
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Add history sharing and accessibility management view
2025-05-14 07:54:36 -04:00
Bjoern Gruening
b2340aa66e
fix NFDI auth
2025-05-13 21:21:22 +02:00
John Chilton
9ff304caf5
Merge pull request #20209 from natefoo/job-execution-package-config-dep
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[24.2] Conditionally import from `galaxy.config` in `galaxy.model.mapping` if `TYPE_CHECKING`
2025-05-13 13:35:29 -04:00
Marius van den Beek
546aee0a58
Merge pull request #20166 from simonbray/replacement-dataset-filter-collection
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Add replacement_dataset option to collection filter tools
2025-05-13 19:28:31 +02:00
John Chilton
631e33f5bd
Merge pull request #19716 from jmchilton/fix_citation_handling
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[24.2] Fix #19515 - invalid citation handling changed with 24.2.
2025-05-13 13:04:22 -04:00
Marius van den Beek
d832488dd9
Merge pull request #20194 from nsoranzo/type_annot_galaxy.model.dataset_collections
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Improve type annotation of ``galaxy.model.dataset_collections``
2025-05-13 17:48:28 +02:00
mvdbeek
665269ce66
Add tools to tool config
2025-05-13 17:47:33 +02:00
Marius van den Beek
9dbe398e82
Merge pull request #19996 from dannon/it-panel
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IT Activity Panel
2025-05-13 16:22:28 +02:00
Marius van den Beek
30bedf3787
Merge pull request #20165 from martenson/aai-updates
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add three AAI providers
2025-05-13 16:18:15 +02:00
Ahmed Awan